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- PDB-3nyk: The structure of cobalt-substituted pseudoazurin from Alcaligenes... -

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Basic information

Entry
Database: PDB / ID: 3nyk
TitleThe structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis
ComponentsPseudoazurin
KeywordsMETAL BINDING PROTEIN / beta-sandwich / red-ox protein / divalent metal-ion / metalloprotein
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.86 Å
AuthorsGessmann, R. / Petratos, K.
CitationJournal: Biopolymers / Year: 2011
Title: The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis.
Authors: Gessmann, R. / Kyvelidou, C. / Papadovasilaki, M. / Petratos, K.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4422
Polymers13,3841
Non-polymers591
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.033, 50.033, 98.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pseudoazurin / Cupredoxin / Blue copper protein


Mass: 13383.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: PAB301 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P04377
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.7
Details: Protein at 5 mg/ml concentration. 50mM Na-citrate pH 5.7, 20 mM CoCl2, 2.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 11, 2010 / Details: Max-Flux mirrors (Osmic Inc.)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→43.33 Å / Num. obs: 11749 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.5
Reflection shellResolution: 1.86→1.93 Å / % possible obs: 98.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 8.8 / Num. measured obs: 1214 / Num. unique all: 1214 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Pattersonsearchmodel building
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
Pattersonsearchphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→43.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.057 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17806 556 4.7 %RANDOM
Rwork0.14956 ---
obs0.1509 11154 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.86→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 1 109 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022987
X-RAY DIFFRACTIONr_bond_other_d0.0010.02936
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9891330
X-RAY DIFFRACTIONr_angle_other_deg1.55932228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6892740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65615207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.415151
X-RAY DIFFRACTIONr_chiral_restr0.0850.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_nbd_refined0.1970.2174
X-RAY DIFFRACTIONr_nbd_other0.1830.2896
X-RAY DIFFRACTIONr_nbtor_refined0.170.2474
X-RAY DIFFRACTIONr_nbtor_other0.0890.2622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4210.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3981.5804
X-RAY DIFFRACTIONr_mcbond_other0.2351.5242
X-RAY DIFFRACTIONr_mcangle_it1.56921003
X-RAY DIFFRACTIONr_scbond_it2.8613435
X-RAY DIFFRACTIONr_scangle_it3.834.5327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 57 -
Rwork0.193 805 -
obs-7106 98.04 %

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